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I did a fatal mistake when upgrading from 1.2.13 to 1..4.1. I actually forgot to to disable plugins and and the wizard told me about them. I was no longer able to access the ACP since all the new 1.4.1 files where uploaded so there was no way for me back except deleting all plugins via FTP and I did so.

Now I am having trouble like settings in the board configuration for a previously working mod with the old version and which was deleted via FTP. I am also having trouble with most plugins since they do not work and some work but with errors.

So is there any possible way to remove all what's 'left' from the old plugins keeping in mind that I am now using 1.4.1?

Thank you very much!

Delete any settings from the plugins you deleted. If you can't do it in the ACP, do it in phpMyAdmin.

And can this be affecting any new plugins I may have been installed?

If you delete setting groups that aren't used by plugins, then there is no harm. Of course there is also no harm in creating a backup before proceeding.